Introduction Fishery is notorious for its high maritime fatalities. Apart from fatal accidents, acute illness without timely emergency medical care may be another important reason for maritime fatalities. However, compared with fatal accidents, maritime fatalities due to acute illness are much less discussed and investigated, and there is need for epidemiological evidence to support and develop preventive strategies.

Methods In Taiwan, Fisheries Agency provided compensation for maritime fatalities, and recorded all enrolled crews in Fishery Administration Management Information System. Using these two databases, incidence rate and odds ratio (OR) were calculated to depict an overall picture of maritime fatalities due to acute illness and associated causal factors.

Results From 2003 to 2015, there were 665 cases of maritime fatalities, whose mechanism were fatal accidents (562, 84.5%) and acute illness (103, 15.5%). Overall incidence rate of maritime fatalities due to acute illness was 0.67 per 10 000 man-labour year. The rates were 0.27, 0.70, and 2.58 per 10 000 man-labour year, and odds ratios were 1.0, 2.60 and 9.65, for coastal (<12 Nautical miles, Nm), inshore (12–200 Nm), and deep sea (>200 Nm) fisheries.

Conclusion Our findings showed that one in seven maritime fatalities is due to acute illness in Taiwanese fishing vessels, and deep sea fisheries had the highest risk, followed by inshore and coastal fisheries, which may be explained by difference in accessibility to emergency medical care. This calls for intervention like regular health screening and occupational health service to prevent the occurrence of acute illness in advance, especially in deep sea fisheries.